Parallel preparation of high fidelity probes in an array format

1. A method for synthesizing an oligonucleotide comprising attaching a linker to a substrate, wherein the linker has a first linker protecting group protecting a first linker reactive group,

removing the first linker protecting group and attaching a first nucleic acid monomer to the first linker reactive group to provide an attached first nucleic acid monomer, wherein the first nucleic acid monomer includes a first reactive group and a first protecting group protecting a first reactive site,

removing the first protecting group and attaching a second nucleic acid monomer to the first reactive site of the first nucleic acid monomer to provide an attached second nucleic acid monomer, wherein the second nucleic acid monomer includes a second reactive group and a second protecting group protecting a second reactive site,

removing the second protecting group and attaching a third nucleic acid monomer to the second reactive site of the second nucleic acid monomer to provide an attached third nucleic acid monomer, wherein the third nucleic acid monomer includes a third reactive group and a third protecting group protecting a third reactive site,

repeating steps of removing a protecting group and attaching a nucleic acid monomer to a reactive site until a desired oligonucleotide is complete,

wherein at least one of the first linker protecting group, first protecting group, second protecting group, third protecting group or protecting group is a compound represented by the following structural formula:

wherein:

X is a nucleic acid monomer;

R 1 and R 2 form a fused aryl ring, R 3 is H; and

Ar is aryl.

2. The method of claim 1 wherein the compound is represented by the following structural formula:

3. The method of claim 1 wherein the compound is represented by the following structural formula:

4. A method for synthesizing an oligonucleotide comprising

attaching a linker to a substrate, wherein the linker has a first linker protecting group protecting a first linker reactive group,

removing the first linker protecting group and attaching a first nucleic acid monomer to the first linker reactive group to provide an attached first nucleic acid monomer, wherein the first nucleic acid monomer includes a first reactive group and a first protecting group protecting a first reactive site,

removing the first protecting group and attaching a second nucleic acid monomer to the first reactive site of the first nucleic acid monomer to provide an attached second nucleic acid monomer, wherein the second nucleic acid monomer includes a second reactive group and a second protecting group protecting a second reactive site,

removing the second protecting group and attaching a third nucleic acid monomer to the second reactive site of the second nucleic acid monomer to provide an attached third nucleic acid monomer, wherein the third nucleic acid monomer includes a third reactive group and a third protecting group protecting a third reactive site,

repeating steps of removing a protecting group and attaching a nucleic acid monomer to a reactive site until a desired oligonucleotide is complete,

wherein at least one of the first linker protecting group, first protecting group, second protecting group, third protecting group or protecting group is a compound represented by the following structural formula:

wherein X is a nucleic acid monomer.

5. The method of claim 1 wherein the oligonucleotide is released from the substrate.

6. The method of claim 5 wherein the oligonucleotide released from the substrate has authentic 3′ hydroxyl termini.

7. The method of claim 1 wherein the linker is a ribonucleotide attached to the substrate as shown below and having a first linker protecting group PG1, second linker protecting group PG2 and base B:

8. The method of claim 1 wherein the first nucleic acid monomer, second nucleic acid monomer, third nucleic acid monomer or nucleic acid monomer has the structure below having a protective group PG, base B and reactive group RG:

9. The method of claim 8 wherein the first reactive group, second reactive group, third reactive group or reactive group is a phosphoramidite reactive group as shown by

wherein R1 is selected from cyanoethyl, methyl, t-butyl, trimethylsilyl or the like, and R2 and R3 are independently selected from isopropyl, cyclohexyl or the like.

10. The method of claim 1 wherein the first reactive site, second reactive site, third reactive site or reactive site is an oxygen atom.

11. The method of claim 8 wherein the B of the structure is G, A, T, or C.

12. The method of claim 1 wherein the oligonucleotide is between about 80 to about 160 nucleotides.

13. The method of claim 4 wherein the oligonucleotide is released from the substrate.

14. The method of claim 13 wherein the oligonucleotide released from the substrate has authentic 3′ hydroxyl termini.

15. The method of claim 4 wherein the linker is a ribonucleotide attached to the substrate as shown below and having a first linker protecting group PG1, second linker protecting group PG2 and base B:

16. The method of claim 4 wherein the first nucleic acid monomer, second nucleic acid monomer, third nucleic acid monomer or nucleic acid monomer has the structure below having a protective group PG, base B and reactive group RG:

17. The method of claim 16 wherein the first reactive group, second reactive group, third reactive group or reactive group is a phosphoramidite reactive group as shown by

wherein R1 is selected from cyanoethyl, methyl, t-butyl, trimethylsilyl or the like, and R2 and R3 are independently selected from isopropyl, cyclohexyl or the like.

18. The method of claim 4 wherein the first reactive site, second reactive site, third reactive site or reactive site is an oxygen atom.

19. The method of claim 16 wherein the B of the structure is G, A, T, or C.

20. The method of claim 4 wherein the oligonucleotide is between about 80 to about 160 nucleotides.